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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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1 <?xml version="1.0"?>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <tool id="FROGS_affiliations_stat" name="FROGS Affiliations stat" version="3.1">
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19 <description>Process some metrics on taxonomies.</description>
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20 <requirements>
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21 <requirement type="package" version="3.1.0">frogs</requirement>
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22 </requirements>
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23 <stdio>
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24 <exit_code range="1:" />
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25 <exit_code range=":-1" />
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26 </stdio>
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27 <command>
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28 affiliations_stat.py
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29 --input-biom $biom
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30 --output-file $summary_file
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31 --rarefaction-ranks $rarefaction_ranks
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32 #if $affiliation.affiliation_type == "FROGS_blast"
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33 --taxonomic-ranks Domain Phylum Class Order Family Genus Species
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34 --multiple-tag "blast_affiliations"
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35 --tax-consensus-tag "blast_taxonomy"
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36 --identity-tag "perc_identity"
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37 --coverage-tag "perc_query_coverage"
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38 #else if $affiliation.affiliation_type == "FROGS_rdp"
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39 --taxonomic-ranks Domain Phylum Class Order Family Genus Species
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40 --taxonomy-tag "rdp_taxonomy"
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41 --bootstrap-tag "rdp_bootstrap"
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42 #else
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43 --taxonomic-ranks $affiliation.taxonomic_ranks
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44 --taxonomy-tag "$affiliation.taxonomy_tag"
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45 #if $affiliation.bootstrap_tag
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46 --bootstrap-tag "$affiliation.bootstrap_tag"
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47 #end if
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48 #if $affiliation.identity_tag and $affiliation.coverage_tag
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49 --identity-tag "$affiliation.identity_tag"
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50 --coverage-tag "$affiliation.coverage_tag"
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51 #end if
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52 #end if
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53 </command>
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54 <inputs>
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55 <!-- Files -->
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56 <param format="biom1" name="biom" type="data" label="Abundance file" help="OTUs abundances and affiliations (format: BIOM)." optional="false" />
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57 <!-- Parameters -->
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58 <param name="rarefaction_ranks" type="text" label="Rarefaction ranks" help="The ranks that will be evaluated in rarefaction. Each rank is separated by one space." optional="false" value="Class Order Family Genus Species" size="80" />
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59 <conditional name="affiliation">
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60 <param name="affiliation_type" type="select" label="Affiliation processed" help="Select the type of affiliation processed. If your affiliation has been processed with an external tool: use 'Custom'.">
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61 <option value="FROGS_blast" selected="true">FROGS blast</option>
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62 <option value="FROGS_rdp">FROGS rdp</option>
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63 <option value="custom">Custom</option>
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64 </param>
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65 <when value="FROGS_blast"></when>
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66 <when value="FROGS_rdp"></when>
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67 <when value="custom">
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68 <param name="taxonomic_ranks" type="text" label="Taxonomic ranks" help="The ordered taxonomic ranks levels stored in BIOM. Each rank is separated by one space." optional="false" value="Domain Phylum Class Order Family Genus Species" size="80" />
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69 <param name="taxonomy_tag" type="text" label="Taxonomy tag" help="The metadata title in BIOM for the taxonomy." optional="false" value="taxonomy" size="20" />
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70 <param name="bootstrap_tag" type="text" label="Bootstrap tag" help="The metadata title in BIOM for the taxonomy bootstrap." value="" size="20" />
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71 <param name="identity_tag" type="text" label="Identity tag" help="The metadata tag used in BIOM file to store the alignment identity." value="" size="20" />
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72 <param name="coverage_tag" type="text" label="Coverage tag" help="The metadata tag used in BIOM file to store the alignment OTUs coverage." value="" size="20" />
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73 </when>
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74 </conditional>
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75 </inputs>
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76 <outputs>
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77 <data format="html" name="summary_file" label="${tool.name}: summary.html" from_work_dir="summary.html"/>
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78 </outputs>
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79 <tests>
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80 <test>
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81 <param name="biom" value="references/06-affiliation.biom" />
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82 <param name="rarefaction_ranks" value="Family Genus Species" />
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83 <conditional name="affiliation">
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84 <param name="affiliation_type" value="FROGS_blast" />
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85 <param name="taxonomic_ranks" value="Domain Phylum Class Order Family Genus Species" />
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86 <param name="taxonomy_tag" value="blast_taxonomy" />
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87 <param name="identity_tag" value="perc_identity" />
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88 <param name="coverage_tag" value="perc_query_coverage" />
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89 <!-- pas de parametre dans le formulaire pour multiple-tag, uniquement une option dans la ligne de commande -->
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90 </conditional>
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91 <output name="summary_file" file="references/09-affiliationsStat.html" compare="sim_size" delta="0" />
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92 <!-- log-file option presente dans la ligne de commande dans le test.sh n'apparait pas du tout ici -->
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93 </test>
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94 </tests>
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95 <help>
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96
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97 .. image:: static/images/frogs_images/FROGS_logo.png
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98 :height: 144
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99 :width: 110
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100
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101
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102 .. class:: infomark page-header h2
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103
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104 What it does
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105
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106 FROGS Affiliations stat computes several metrics and generates a HTML file describing OTUs based on their taxonomies and the quality of the affiliations.
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107
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108
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109 .. class:: infomark page-header h2
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110
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111 Input/output
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112
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113 .. class:: h3
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114
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115 Input
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116
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117 **Abundance file**:
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118
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119 The abundance and affiliation of each OTUs in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_). This file can be produced by FROGS Affiliation OTU.
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120
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121 The FROGS's tools working on clusters and others metagenomic workflows produce files in BIOM format.
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122
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123 .. class:: h3
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124
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125 Output
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126
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127 **Summary file** (summary.html):
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128
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129 OTUs taxonomies and affiliations metrics (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_):
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130
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131 *-Taxonomy distribution*: display the distribution of each taxon and the rarefaction for each taxonomic rank and for each sample
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132
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133 .. image:: static/images/frogs_images/FROGS_affiliation_stat_taxonomies.png
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134 :height: 380
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135 :width: 650
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136
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137 .. image:: static/images/frogs_images/FROGS_affiliation_stat_rarefaction.png
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138 :height: 380
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139 :width: 550
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140
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141 .. image:: static/images/frogs_images/FROGS_affiliation_stat_sunburst.png
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142 :height: 380
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143 :width: 430
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144
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145 -Bootstrap distribution: display for affiliation methods with bootstrap the bootstrap on each taxonomic rank
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146
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147 .. image:: static/images/frogs_images/FROGS_affiliation_stat_bootstrap.png
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148 :height: 380
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149 :width: 650
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150
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151 -Alignment distribution: display for affiliation methods with alignment the distribution of identity/covrage
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152
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153 .. image:: static/images/frogs_images/FROGS_affiliation_stat_alignment.png
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154 :height: 380
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155 :width: 650
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156
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157
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158
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159 ----
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160
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161 **Contact**
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162
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163 Contacts: frogs@inra.fr
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164
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165 Repository: https://github.com/geraldinepascal/FROGS
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166 website: http://frogs.toulouse.inra.fr/
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167
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168 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
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169
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170 </help>
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171 <citations>
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172 <citation type="doi">10.1093/bioinformatics/btx791</citation>
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173 </citations>
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174
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175 </tool>